{"id":18621296,"url":"https://github.com/4ment/torchtree-experiments","last_synced_at":"2026-04-29T10:03:12.361Z","repository":{"id":206885302,"uuid":"716908709","full_name":"4ment/torchtree-experiments","owner":"4ment","description":null,"archived":false,"fork":false,"pushed_at":"2026-04-23T09:28:50.000Z","size":174,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-04-23T11:26:31.290Z","etag":null,"topics":["phylogenetics","physher","pytorch","torchtree","variational-bayes"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/4ment.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-11-10T06:01:38.000Z","updated_at":"2026-04-23T09:28:54.000Z","dependencies_parsed_at":"2024-03-21T06:31:33.622Z","dependency_job_id":"2e7d6d69-4479-4b4d-b299-1e9819c10f6f","html_url":"https://github.com/4ment/torchtree-experiments","commit_stats":null,"previous_names":["4ment/torchtree-experiments"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/4ment/torchtree-experiments","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Ftorchtree-experiments","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Ftorchtree-experiments/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Ftorchtree-experiments/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Ftorchtree-experiments/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/4ment","download_url":"https://codeload.github.com/4ment/torchtree-experiments/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Ftorchtree-experiments/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32420356,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-29T06:29:02.080Z","status":"ssl_error","status_checked_at":"2026-04-29T06:29:00.631Z","response_time":110,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["phylogenetics","physher","pytorch","torchtree","variational-bayes"],"created_at":"2024-11-07T04:10:21.364Z","updated_at":"2026-04-29T10:03:12.327Z","avatar_url":"https://github.com/4ment.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# torchtree-experiments\n\n[![Docker Image CI](https://github.com/4ment/torchtree-experiments/actions/workflows/docker-image.yml/badge.svg)](https://github.com/4ment/torchtree-experiments/actions/workflows/docker-image.yml)\n\nThis repository contains the pipeline and data supporting the results of the following article:\n\nMathieu Fourment, Matthew Macaulay, Christiaan J Swanepoel, Xiang Ji, Marc A Suchard, Frederick A Matsen IV. torchtree: flexible phylogenetic model development and inference using PyTorch. [arXiv:2406.18044](https://arxiv.org/abs/2406.18044)\n\n## Data\n\n### SARS-CoV-2\nWe reproduce the SARS-CoV-2 analysis perfomed by [Magee _et al._, 2023](https://arxiv.org/abs/2303.13642). Detailed information on installing the appropriate versions of BEAST and BEAGLE is available on their GitHub [repository](https://github.com/suchard-group/approximate_substitution_gradient_supplement).\nDue to data sharing limitations, sequences need to be downloaded from GISAID and the alignment (FASTA format) needs to be provided to the pipeline. The GISAID accession IDs are available in [acknowledgements_table.xlsx](https://github.com/suchard-group/approximate_substitution_gradient_supplement/blob/main/acknowledgements_table.xlsx).\n\n## Dependencies\nTo execute this pipeline, it is necessary to install [nextflow](https://www.nextflow.io). [Docker](https://www.docker.com) is not required but it is highly recommended to use it due to the numerous dependencies.\n\n## Installation\n\n    git clone 4ment/torchtree-experiments.git\n    cd torchtree-experiments/\n    chmod +x bin/*.py\n\n## Pipeline without docker/singularity\n\n### Installing dependencies with conda\n    conda env create -f environment.yml\n    conda activate torchtree-experiments\n    \n    RUN wget https://github.com/4ment/physher/archive/refs/tags/v2.0.1.tar.gz\n    tar -xzvf v2.0.1.tar.gz\n    cmake -S physher-2.0.1 -B physher-2.0.1/build -DBUILD_CPP_WRAPPER=on -DBUILD_TESTING=on -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX/envs/torchtree-experiments\n    cmake --build physher-2.0.1/build/ --target install\n    export LIBRARY_PATH=$LIBRARY_PATH:$CONDA_PREFIX/envs/torchtree-experiments/lib\n\n    pip install torch==1.12.1 numpy==1.22 torchtree==1.0.2\n    pip install torchtree-physher==1.0.0 torchtree-scipy==1.0.0\n\n### Running the pipeline\n\n    nextflow run main.nf -profile conda --sc2 sc2.fa\n\n`sc2.fa` is the sequence alignment file containing the SARS-CoV-2 sequences (see [SARS-CoV-2](#sars-cov-2) section for more details)\n\n## Pipeline with docker or singularity\nThere is no need to install dependencies with docker or singularity.\n\n### Running the pipeline with docker\n\n    nextflow run main.nf -profile docker --sc2 sc2.fa\n\n### Running the pipeline with singularity and PBS\n\n    nextflow -C configs/uts.config run main.nf -profile singularity --sc2 sc2.fa\n\nSince the pipeline will take weeks to run to completion one should use a high performance computer. An example of configuration file for PBS Pro can be found in the [configs](configs/) folder.\n\n## Summarizing results\n\nAll R packages used for plotting the results can be installed using renv. This command needs to be run only once.\n\n    Rscript -e 'renv::restore()'\n\nGenerate figures in a single pdf:\n\n    Rscript -e 'rmarkdown::render(\"index.Rmd\")'\n\nNote:\n\nrmarkdown requires pandoc to be installed. The conda environment provided in this repo includes pandoc.\nIt is also possible to use RStudio to run the `index.Rmd` script.\n\n\n## Program and library versions\n\nFor reproducibility, we provide below the version of each library/program used in the benchmark.\n\n| Program/Library | Version |\n| --------------- | ------- |\n| [physher]           | 2.0.1 |\n| [torchtree]         | 1.0.2 |\n| [torchtree-physher] | 1.0.0 |\n| [torchtree-scipy]   | 1.0.0 |\n| [pytorch]           | 1.12.1 |\n\n\nThe R scripts use the [skyplotr] package, and it is downloadable using [devtools](https://github.com/hadley/devtools):\n\n    Rscript -e 'devtools::install_github(\"4ment/skyplotr\", ref=\"8abc10a\")'\n\n\n[physher]: https://github.com/4ment/physher\n[torchtree]: https://github.com/4ment/torchtree\n[torchtree-physher]: https://github.com/4ment/torchtree-physher\n[torchtree-scipy]: https://github.com/4ment/torchtree-scipy\n[skyplotr]: https://github.com/4ment/skyplotr\n\n[PyTorch]: https://pytorch.org","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Ftorchtree-experiments","html_url":"https://awesome.ecosyste.ms/projects/github.com%2F4ment%2Ftorchtree-experiments","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Ftorchtree-experiments/lists"}